Objectives and subtitles would originally appear at the centre of the screen and then move up. This was changed to have them only appear at the top, as presumably the original idea was too distracting.
Colton was originally named Seth, and Ned was Seth's uncle instead of his adopted father.
Sadie was also not originally going to die on the Morning Star; instead, Ned sends Seth to look for her at the Alhambra, and Jenny tells Seth that she doesn't work there anymore.
A mission with the Kragen Gang was cut from the main story for unknown reasons, but eventually was added back to the PSP rerelease, Gun Showdown.
Test maps exist for multiplayer, including team deathmatch. This was also cut, but multiplayer was reinstated in Showdown.
The original title of the Whore Coach mission implies that Cole/Seth would be escorting Sadie and Jenny out of the Alhambra instead of just Jenny.
Quickdraw originally worked more like Deadeye, where Cole zoomed in to a tight over-the-shoulder view while picking off enemies in slow motion, and it could be used with any weapon.
Cole's death animations originally had Ludicrous Gibs, including juicy headshots. The final game tones this down considerably, with limbs flying off only if Cole dies in an explosion.
shows that parts of the game were considerably different.